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RamanLab / fbc_curation_matlab

fbc_curation contains MATLAB/COBRA helpers for reproducibility of fbc models.
GNU Lesser General Public License v3.0
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fbc_curation_matlab

fbc_curation_matlab contains MATLAB/COBRA helpers for checking reproducibility of fbc models.

Pre-requisites

Components in the repository

Installation

  1. Clone the repository to your system.
  2. Extract the folders.
  3. Add the folders to you MATLAB path using addpath(genpath(path to fbc_curation_matlab))
  4. Installation is complete!

Usage

Step 1: Initialize CobraToolBox using the command 

initCobraToolbox

fbc_curation_matlab uses functions from CobraToolBox. So it has to be initialized every time MATLAB is started. Running this command once every session is enough.

Step 2: Running FBC-curation

run_FROG(path to model)

Step 2 with FBC Curator name

run_FROG(path to model, curator_name)

This command will start the fbc curation and FROG report files will be available in the current directory as COMBINE archive format. It is basically a zip file with all the report files in a specific file structure.

Verify installation

To make sure if the tool is installed properly, run the following command.

run_FROG(path to fbc_curation_matlab/src/fbc_curation/examples/models/e_coli_core.xml)

If the command runs and give the following output without any error. The installation is successfull.

Using gurobi solver.
Loading model from e_coli_core.xml... Elapsed time is 3.178258 seconds.
Created directory ./FROG successfully.
[00] Wrote Metadata details to FROG/metadata.json.
[01] Wrote FBA objective results to FROG/01_objective.tsv.
[02] Wrote FVA results (optPercentage = 100) to FROG/02_fva.tsv.
Single gene deletion analysis in progress ...
100%    [........................................]
[03] Wrote gene deletion results to FROG/03_gene_deletion.tsv.
Single reaction deletion analysis in progress ...
100%    [........................................]
[04] Wrote gene deletion results to FROG/04_reaction_deletion.tsv.
Total Elapsed time is 4.759139 seconds.
Created COMBINE archive file ./e_coli_core.zip successfully.
e_coli_core.zip file renamed to ./e_coli_core.omex successfully.

Example Output

>> run_FROG('fbc_curation_matlab-main/src/fbc_curation/examples/models/iJR904.xml', 'Karthik Raman');
Using glpk solver.
Loading model from fbc_curation_matlab-main/src/fbc_curation/examples/models/iJR904.xml... Elapsed time is 39.618113 seconds.
Created directory ./FROG successfully.
FROG curator name:Karthik Raman
[00] Wrote Metadata details to FROG/00_metadata.json.
[01] Wrote FBA objective results to FROG/01_objective.tsv.
[02] Wrote FVA results (optPercentage = 100) to FROG/02_fva.tsv.
Single gene deletion analysis in progress ...
100%    [........................................]
[03] Wrote gene deletion results to FROG/03_gene_deletion.tsv.
Single reaction deletion analysis in progress ...
100%    [........................................]
[04] Wrote gene deletion results to FROG/04_reaction_deletion.tsv.
Total Elapsed time is 111.763478 seconds.
Created COMBINE archive file ./iJR904.zip successfully.
iJR904.zip file renamed to ./iJR904.omex successfully.
>>

See the files in fbc_curation/examples/results/ for how the output files look like.

Possible minor issues and troubleshooting

License

fbc_curation_matlab source is released under both the GPL and LGPL licenses version 2 or later. You may choose which license you choose to use the software under.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License or the GNU Lesser General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Acknowledgements

© 2020 Karthik Raman